"
Team:UANL Mty-Mexico/Modeling/3Dmodel/Metal-binding
From 2012.igem.org
(Difference between revisions)
Mariotrevino (Talk | contribs) |
|||
| (7 intermediate revisions not shown) | |||
| Line 3: | Line 3: | ||
<div class="content"> | <div class="content"> | ||
| - | <p><br><h3> | + | <p><br><h3>Metal-binding Behaviour</h3></p> |
<br> | <br> | ||
| + | <p><b>Methodology</b></p> | ||
| + | <br> | ||
| + | |||
| + | <p>We used the FoldX force field (Schymkowitz et al. 2005) to predict the metal-binding sites and energies of the predicted partial tertiary structure of rhM. The ionic strength, and pH were adjusted in order to simulate the experimental conditions, we tested the following algorithm replacing the field [M] (6th line) with the atoms Ca, Mg, Mn, Na, Zn, Fe, Cu, Co, K, also considering the changes in the ionic strength.</p> | ||
| + | <br> | ||
| + | |||
| + | <table class="image" align="center"> | ||
| + | <caption align="bottom">.</caption> | ||
| + | <tr><td><img src="https://static.igem.org/mediawiki/2012/1/16/UANLDCSelection_006.png" style="width:300px;"></td></tr> | ||
| + | </table> | ||
| + | <br> | ||
| + | |||
| + | <p><b>Results</b></p> | ||
| + | <br> | ||
| + | |||
| + | <p>The algorithm described above did not predict any metal-binding site. Presumably due to the lack of “precision” of the partial model. We expect to obtain metalbinding sites by obtaining more accurate models of rhMT.</p> | ||
| + | <br> | ||
| Line 15: | Line 32: | ||
<a href="https://2012.igem.org/Team:UANL_Mty-Mexico/Modeling/3Dmodel"><li>Overview</a></li> | <a href="https://2012.igem.org/Team:UANL_Mty-Mexico/Modeling/3Dmodel"><li>Overview</a></li> | ||
<a href="https://2012.igem.org/Team:UANL_Mty-Mexico/Modeling/3Dmodel/structure_prediction"><li>Structure Prediction</a></li> | <a href="https://2012.igem.org/Team:UANL_Mty-Mexico/Modeling/3Dmodel/structure_prediction"><li>Structure Prediction</a></li> | ||
| - | + | ||
<a href="https://2012.igem.org/Team:UANL_Mty-Mexico/Modeling/3Dmodel/Metal-binding"><li><b>>>Metal-binding Behaviour</b></a></li> | <a href="https://2012.igem.org/Team:UANL_Mty-Mexico/Modeling/3Dmodel/Metal-binding"><li><b>>>Metal-binding Behaviour</b></a></li> | ||
<a href="https://2012.igem.org/Team:UANL_Mty-Mexico/Modeling/3Dmodel/references"><li>References</a></li> | <a href="https://2012.igem.org/Team:UANL_Mty-Mexico/Modeling/3Dmodel/references"><li>References</a></li> | ||
Latest revision as of 03:51, 27 September 2012
Metal-binding Behaviour
Methodology
We used the FoldX force field (Schymkowitz et al. 2005) to predict the metal-binding sites and energies of the predicted partial tertiary structure of rhM. The ionic strength, and pH were adjusted in order to simulate the experimental conditions, we tested the following algorithm replacing the field [M] (6th line) with the atoms Ca, Mg, Mn, Na, Zn, Fe, Cu, Co, K, also considering the changes in the ionic strength.
 |
Results
The algorithm described above did not predict any metal-binding site. Presumably due to the lack of “precision” of the partial model. We expect to obtain metalbinding sites by obtaining more accurate models of rhMT.
